Chemistry of Life: video

Showing posts with label video. Show all posts

12/24/2007

ATPases

ATP synthase is the final enzyme of oxidative phosporylation. It is located in the mitochondrial membrane and utilizes the potential energy generated by an electron transfer chain to phosphorylate ADP to ATP.

Harvard University provides a wonderful video explaining operation of the F1-F0 ATPase.

12/07/2007

replication

Replication results in the copy of the DNA double helix, and, like transcription, proceeds 3' to 5' on the template strand and 5' to 3' on the replica strand. Replication is "semi-conservative" in that each new DNA double helix contains one of the original "parental" strands along with a newly synthesized strand.

Other possibilities for replication would have been
1. Fully conservative replication, with an original parental strand plus a complete new double stranded copy, or
2. Fully nonconservative replication ("dispersive") with disassembly, copying of fragments, and reassembly into two new randomly mixed strands each containing sections of the original and copied segments.)

Helicases are a critical part of the DNA replication process because they unwind double-stranded DNA to create single strands suitable for copying by the replication machinery. This and other helicase activity in the cell depends on the ability of the helicase's protein “engine” to crawl along the DNA strand. This locomotion is powered by ATP, the cell's ubiquitous energy source. Helicase ProteinA helicase protein moves rapidly on a highly flexible single-stranded DNA track. Repetitive movement on the DNA may keep it clear of potentially toxic proteins. Watch Animation 8KB Flash Animation(requires Flash Player)

Rediscovering Biology - Genomics Animations and Images - Genetics of Development - Animations and Images - Biology of Sex & Gender - Animations and Images - Genetically modified organisms - Animations and Images - Biodiversity - Animations and Images :

12/05/2007

transcription

The wonders of a tiny cell

Transcription (Animation) : Transcription : DNA : Journey of the Nucleotides : Lodish et al 2000 Gene Expression : Bio DNA RNA Aminoacid part 1 of 2 : Bio DNA RNA Aminoacid part 2 of 2 : Straddling on DNA: Human TFIIA/TBP/DNA Complex : DNA RNA : Transcription and Translation :

In transcription, an RNA polymerase enzyme (RNAp, or pol III in eukaryotes) directs generation of a complementary strand of mRNA from DNA. The mechanism of alternative splicing enables to production of different mature mRNA molecules, depending on what sequences are treated as introns and what remain as exons. The rate of gene transcription is controlled by complex interactions between cis-acting elements within regulatory DNA sequences and trans-acting factors, including transcription factors and the basal transcription complex, which comprises the RNA polymerase and proteins necessary for correct initiation and elongation.

Transcription, like replication, proceeds 3' to 5' on the template strand and 5' to 3' on the new strand.

Transcription involves 3 phases: initiation, elongation, and termination.
1. Having bound to the promoter region , RNA polymerase II initiates transcription at the first nucleotide of the first exon of a class II gene (PIC).
2. The 5' end of the nascent RNA is capped with 7-methylguanylate (capping).
3. Transcription by RNA polymerase II terminates at any one of multiple termination sites downstream from the poly(A) site, which is located at the 3' end of the final exon.
4. After the primary transcript is cleaved at the poly(A) site.
5. A string of adenine (A) residues is added (polyadenylation). The poly(A) tail contains ≈250 A residues in mammals, ≈150 in insects, and ≈100 in yeasts.

Find on/off : Find start : Find stop :

In more detail:
RNA polymerase binds to the promoter region of one strand of DNA (5’ end), and the DNA double helix is un-zipped into single strands. First, RNA polymerase requires a number of general transcription factors (called TFIIA, TFIIB, etc.). Many promoters contain a DNA sequence called the TATA box, which is located 25 nucleotides away from the site of initiation of transcription. The TATA box is recognized and bound by transcription factor TFIID, which then enables the adjacent binding of TFIIB. The rest of the general transcription factors plus the RNA polymerase assemble at the promoter. diagram - initiation of transcription.

The RNAp enzyme moves toward the 3’ end, connecting complementary bases into an elongating chain of RNA nucleotides. At termination, the transcribed mRNA molecule is released from the DNA strand. In prokaryotic cells – without a nuclear membrane – translation may begin prior to termination. In eukaryotic cells – with a nuclear membrane – the processed mRNA moves through the nuclear pores into the cytoplasm, where ribosomes on the rough endoplasmic reticulum translate the mRNA code into a peptide or a protein. Epigenetic, alternative splicing mechanisms can edit the mRNA prior to its translation into protein.

Capping of the 5’ end on the pre-mRNA with 7-methylguanylate occurs soon after initiation of transcription, and the 5 cap is retained in mature mRNAs.

Cleavage, pre-mRNA splicing, and polyadenylation usually follow termination of transcription of short primary transcripts with few introns. However, introns often are spliced out of the nascent RNA before transcription of the gene is complete for large genes with multiple introns.

It was believed that most genes in higher eukaryotes are regulated by controlling their transcription. However, it is increasingly recognized that epigenetic mechanisms (such as alternative splicing) are important in generating many proteins from a single gene, accounting for the Human Genome Project’s discovery that a mere 30,000 genes code for about 100,000 proteins.

animation - start of transcription : animation - life cycle of an mRNA : animation ~ alternative splicing : ball-stick - dna double helix : animation - adenine tyrosine H bonds : animation - cytosine guanine H bonds :

More at NCBI Molecular Cell Biology - Transcription Initiation Complex : SUMMARY transcription initiation (NCBI MCB) : Processes of Transcription : Wikipedia : Central Dogma :

translation

Protein Translation

More YouTube Videos: From RNA to Protein Synthesis : Protein synthesis: an epic on the cellular level : Translation : Protein Translation

Coding instructions of nucleotide sequences in archival DNA, which have been transcribed and processed into mRNAs are translated into polypeptides and proteins at cytoplasmic ribosomes. Translation is the ultimate step in gene expression, in which archival genetic instructions are converted into sequences of amino acids in peptides, polypeptides, and proteins.

Analogous with transcription, translation incorporates initiation (usually cap-dependent activation-initiation in eukaryotes), elongation, and termination steps:

Initiation – Aminoacyl-tRNAs carrying specific amino acids pair with the corresponding mRNA codons at the ribosome. Here, base pairing (A-U, C-G) between triplet mRNA codons and complementary tRNA anticodons ensures the coded insertion of amino acids into a protein sequence (primary structure).

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). Most eukaryotic mRNAs require the cap-binding complex elF4F for efficient initiation of translation, which occurs as a result of ribosomal scanning from the capped 5' end of the mRNA to the initiation codon. Initiator tRNA, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the initiation codon of mRNA.

The cap-binding complex eIF4F and the factors eIF4A and eIF4B are necessary for binding of 43S complexes (comprising a 40S subunit, eIF2/GTP/Met-tRNAi and eIF3) to the 5' end of capped mRNA yet are not sufficient to promote ribosomal scanning to the initiation codon. The cap-binding factor eIF1A enhances the ability of eIF1 to dissociate aberrantly assembled complexes from mRNA, and these factors synergistically mediate 48S complex assembly at the initiation codon. The joining of 48S complexes to 60S subunits to form 80S ribosomes requires eIF5B, which has an essential ribosome-dependent GTPase activity and hydrolysis of eIF2-bound GTP induced by eIF5. Initiation on a few mRNAs is cap-independent and occurs instead by internal ribosomal entry.

The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. The physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site.[s] In eubacteria, base pairing between the 3' end of 16S rRNA and the ribosome-binding site of mRNA is required for efficient initiation of translation. A few cellular and viral mRNAs are translated by a cap and end-independent mechanism known as internal ribosomal entry. Ribosome shunting, or the ribosomal shunt initiation pathway is an alternate viral mechanism of translation initiation in which ribosomes bind to the mRNA in a normal cap-dependent mode, then jump upstream (5') of the initiator AUG codon.

Through the cap-dependent process:
1. The mRNA start codon forms an initiation complex with both the small ribosomal subunit and with initiator tRNA (carrying the amino acid methionine). In this step, the Met-tRNAi forms a base pair with the start codon at the P site – a second aminoacylated tRNA will subsequently bind to the adjacent A site during elongation.

The start codon is usually AUG, but prokaryotes may utilize alternative start codons, or insert N-Formylmethionine. The small subunit of the ribosome binds to 5' end of mRNA with the help of initiation factors (IF). Next, the large ribosomal subunit joins this complex to enable elongation.

2. Elongation – amino acids are added to the growing polypeptide chain as each tRNA delivers its amino acid, forming a complex with elongation factor (EF) and GTP. The amino acid is transferred from the tRNA to the mRNA, moving from the P site to the A site. Next, the peptidyl tRNA vacates the A site and moves to the P site, leaving the A site available for the next amino acid-carrying tRNA. Amino acids are joined by peptide bonds as carboxyl group are added to the 3' OH by an ester bond. The ribosome acts as an enzyme (ribozyme) in the formation of the peptide bond.

3. Termination – elongation of the polypeptide chain ceases when the ribosomal machine encounters a nonsense (stop) codon (UAA, UGA, or UAG). The newly assembled polypeptide is released from the ribosomal machine when the ribosome breaks into its large and small subunits, releasing both the polypeptide and its mRNA.

Each mRNA that codes for a specific polypeptide chain may be utilized hundreds of times before it is degraded (destroyed by nonstop decay) by the cell. Such degradation of proto-oncogene mRNA is essential for avoidance of unchecked proliferation and carcinogenesis. Some antibiotics act by disrupting prokaryotic translation.